If you're using the Intuit Online Payroll subscription, you need to create a separate bonus paycheck to see the options for tax settings. Let me show you how:
Select the Payday tab.
From the Check Type drop-down, select Bonus Checks.
Select the applicable settings for the bonus paycheck.
Pick the employee, then enter the amount in the Bonus field.
Click Create and ApprovePaychecks button.
To check which option to select in the Settings section, the following article contains the requirements when to select Supplemental tax, Net-to-gross calculation, or Include retirement account deductions, contributions, and garnishment: Pay an employee bonus. The steps and information outlined in this article are for both Intuit Online and QuickBooks Online Payroll subscriptions.
However, if you're using the Desktop version, you have three options to pay bonuses to employees. The taxability of the bonus paychecks depends on the method you've chosen.